Could you please eloborate more
* What does the package contains?
* What was folder structure before install?
* What is not deleting after uninstall?
Package contains project folder for example: /apps/<myproject>, along with some the folders
Folder structure will be /apps/<myproject>
After uninstalling a package, under /apps nothing is deleted.
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Uninstalling package means it will revert it to previous version. If nothing was installed before then it will delete folder structure.
It's worth noting that I've had trouble with the "revert" part of that in 5.4, as this post is tagged. It seems to be better with 5.5.